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2WW3
Biol. Unit 5
Info
Asym.Unit (745 KB)
Biol.Unit 1 (132 KB)
Biol.Unit 2 (130 KB)
Biol.Unit 3 (134 KB)
Biol.Unit 4 (130 KB)
Biol.Unit 5 (132 KB)
Biol.Unit 6 (131 KB)
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(1)
Title
:
STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT3990 FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 IN COMPLEX WITH THIOMANNOBIOSIDE
Authors
:
M. D. L. Suits, Y. Zhu, A. J. Thompson, H. J. Gilbert, G. J. Davies
Date
:
21 Oct 09 (Deposition) - 26 Jan 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
Hydrolase, Glycoside Hydrolase Family 92, Gh92, Bt3990
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhu, M. D. L. Suits, A. J. Thompson, S. Chavan, Z. Dinev, C. Dumon, N. Smith, K. W. Moremen, Y. Xiang, A. Siriwardena, S. J. Williams, H. J. Gilbert, G. J. Davies
Mechanistic Insights Into A Ca(2+)-Dependent Family Of Alpha-Mannosidases In A Human Gut Symbiont.
Nat. Chem. Biol. V. 6 125 2010
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDa)
3b: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDb)
3c: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDc)
3d: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDd)
3e: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDe)
3f: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
1
Ligand/Ion
GLYCEROL
3
SMD
1
Ligand/Ion
METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO-ALPHA-D-MANNOPYRANOSIDE
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Sites
(3, 3)
Info
All Sites
1: BC2 (SOFTWARE)
2: BC3 (SOFTWARE)
3: BC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
BC2
SOFTWARE
ASP E:348 , GLN E:602 , ASP E:644 , SMD E:801 , HOH E:2148 , HOH E:2149
BINDING SITE FOR RESIDUE CA E 800
2
BC3
SOFTWARE
SER E:86 , TRP E:88 , ILE E:89 , TRP E:347 , ASP E:348 , TRP E:385 , MET E:394 , GLU E:533 , HIS E:584 , GLU E:585 , GLN E:602 , ASP E:642 , ASP E:644 , CA E:800
BINDING SITE FOR RESIDUE SMD E 801
3
BC4
SOFTWARE
GLN E:284 , LYS E:288 , TYR E:361 , VAL E:364 , GLU E:684 , HOH E:2217
BINDING SITE FOR RESIDUE GOL E 802
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
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CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_2ww3A02 (A:289-312,A:607-631,A:632-748)
1b: CATH_2ww3B02 (B:289-312,B:607-631,B:632-748)
1c: CATH_2ww3C02 (C:289-312,C:607-631,C:632-748)
1d: CATH_2ww3D02 (D:289-312,D:607-631,D:632-748)
1e: CATH_2ww3E02 (E:289-312,E:607-631,E:632-748)
1f: CATH_2ww3F02 (F:289-312,F:607-631,F:632-748)
2a: CATH_2ww3A03 (A:344-438)
2b: CATH_2ww3B03 (B:344-438)
2c: CATH_2ww3C03 (C:344-438)
2d: CATH_2ww3D03 (D:344-438)
2e: CATH_2ww3E03 (E:344-438)
2f: CATH_2ww3F03 (F:344-438)
3a: CATH_2ww3A01 (A:20-53,A:54-288,A:313-343)
3b: CATH_2ww3B01 (B:20-53,B:54-288,B:313-343)
3c: CATH_2ww3C01 (C:20-53,C:54-288,C:313-343)
3d: CATH_2ww3D01 (D:20-53,D:54-288,D:313-343)
3e: CATH_2ww3E01 (E:20-53,E:54-288,E:313-343)
3f: CATH_2ww3F01 (F:20-53,F:54-288,F:313-343)
View:
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)
(
)
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(
)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
GH92 mannosidase fold
(8)
Homologous Superfamily
:
GH92 mannosidase domain
(8)
Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482.
(8)
1a
2ww3A02
A:289-312,A:607-631,A:632-748
1b
2ww3B02
B:289-312,B:607-631,B:632-748
1c
2ww3C02
C:289-312,C:607-631,C:632-748
1d
2ww3D02
D:289-312,D:607-631,D:632-748
1e
2ww3E02
E:289-312,E:607-631,E:632-748
1f
2ww3F02
F:289-312,F:607-631,F:632-748
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
(267)
Homologous Superfamily
:
alpha-1,2-mannosidase
(8)
Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482.
(8)
2a
2ww3A03
A:344-438
2b
2ww3B03
B:344-438
2c
2ww3C03
C:344-438
2d
2ww3D03
D:344-438
2e
2ww3E03
E:344-438
2f
2ww3F03
F:344-438
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
[code=2.70.98.10, no name defined]
(116)
Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482.
(8)
3a
2ww3A01
A:20-53,A:54-288,A:313-343
3b
2ww3B01
B:20-53,B:54-288,B:313-343
3c
2ww3C01
C:20-53,C:54-288,C:313-343
3d
2ww3D01
D:20-53,D:54-288,D:313-343
3e
2ww3E01
E:20-53,E:54-288,E:313-343
3f
2ww3F01
F:20-53,F:54-288,F:313-343
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_92_2ww3F01 (F:228-737)
1b: PFAM_Glyco_hydro_92_2ww3F02 (F:228-737)
1c: PFAM_Glyco_hydro_92_2ww3F03 (F:228-737)
1d: PFAM_Glyco_hydro_92_2ww3F04 (F:228-737)
1e: PFAM_Glyco_hydro_92_2ww3F05 (F:228-737)
1f: PFAM_Glyco_hydro_92_2ww3F06 (F:228-737)
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)
Clan
:
Pec_lyase
(42)
Family
:
Glyco_hydro_92
(7)
Bacteroides thetaiotaomicron
(7)
1a
Glyco_hydro_92-2ww3F01
F:228-737
1b
Glyco_hydro_92-2ww3F02
F:228-737
1c
Glyco_hydro_92-2ww3F03
F:228-737
1d
Glyco_hydro_92-2ww3F04
F:228-737
1e
Glyco_hydro_92-2ww3F05
F:228-737
1f
Glyco_hydro_92-2ww3F06
F:228-737
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Asymmetric Unit 1
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Asym.Unit (745 KB)
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